[gmx-users] Expanded Ensemble and Gromacs 4.6

[Michael Shirts]

Hi, Joakim-

Expanded ensemble is still a bit experimental.  I don't immediately
see any problem that jump right out, but if you go to
http://redmine.gromacs.org/ and file a bug report, including giving
example files that cause the problem, I can take a look at it.

On Tue, Feb 5, 2013 at 6:00 AM, Joakim Jämbeck <jambeck at me.com> wrote:
> Hi,
>
> I am trying to use the Expanded Ensemble (EE) method to compute the free energy of solvation of a small organic molecule.
>
> Basically I am playing around but I cannot get the simulations to run.
>
> Here are my EE and free energy settings:
>
> %-------------------------------------------------------
> free-energy             = expanded      ; Expanded ensemble
> couple-moltype          = C1X           ; Molecule to introduce
> couple-lambda0          = none          ; Go from no interactions with solvent...
> couple-lambda1          = vdw-q         ; ...to full interactions
> couple-intramol         = no            ; Do not decouple internal interactions
> init_lambda_state       = 0             ; Start from the first column of the lambda vectors
> delta-lambda            = 0             ; No increments in lambda
> nstdhdl                 = 100           ; Frequency for writing dH/dlambda
> coul-lambdas            = 0.0 0.25 0.5 0.75 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> vdw-lambdas             = 0.0 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.7 0.8 0.9 1.0
> dhdl-print-energy       = yes           ; Include total energy in the dhdl file
> sc-alpha                = 0.5           ; Soft core alpha parameter
> sc-power                = 1             ; Power of lambda in soft core function
> sc-r-power              = 6             ; Power of radial term in the soft core function
> sc-sigma                = 0.3           ; Soft core sigma
> sc-coul                 = no            ; No soft core for Coulomb
> separate-dhdl-file      = yes           ; Seperate dhdl files
> dhdl-derivatives        = yes           ; Print derivatives of the Hamiltonian
>
> ; expanded ensemble variables
> nstexpanded             = 100           ; Number of steps between attempts to change the Hamiltonian
> lmc-stats               = wang-landau   ; WL algorithm to explore state space
> lmc-move                = gibbs         ; Decides which state to move to
> lmc-weights-equil       = number-steps  ; EE weight updating stops after...
> weight-equil-number-steps = 5000000     ; ...10ns of simulation
>
> ; Seed for Monte Carlo in lambda space
> lmc-seed                = 1993
> lmc-repeats             = 1
> lmc-gibbsdelta          = -1
> lmc-forced-nstart       = 0
> symmetrized-transition-matrix = no
> nst-transition-matrix   = -1
> mininum-var-min         = 100
> wl-scale                = 0.6
> wl-ratio                = 0.8
> init-wl-delta           = 1
> wl-oneovert             = yes
> %-------------------------------------------------------
>
> Besides this I use LINCS to constrain all bonds, sd-integrator and a "normal" cut-off scheme with a 1 fs time step.
>
> However, once I try to run the files on the cluster I always end up with LINCS warnings and after a few seconds the program crashes due to too many LINCS warnings. If I increase the time step to 2 fs I run into problems SETTLE for the water. I always start from a nice structure that is taken as the final snap shot from a simple 1 ns MD simulation of my system.
>
> What could be the problem?
>
> If I use free_energy = yes instead of EE things work fine.
>
> Did I perhaps mess up the EE settings or something?
>
> Thanks in advance.
>
> Best,
> Joakim
>
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